GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Sulfurivirga caldicuralii DSM 17737

Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_074201116.1 BUQ81_RS04050 glutamate-1-semialdehyde 2,1-aminomutase

Query= BRENDA::Q93R93
         (395 letters)



>NCBI__GCF_900141795.1:WP_074201116.1
          Length = 432

 Score =  169 bits (429), Expect = 1e-46
 Identities = 111/294 (37%), Positives = 153/294 (52%), Gaps = 19/294 (6%)

Query: 29  LLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPM 88
           + I R +GA VWD +G  YID VG +G A LGH +PEVVEAV++QAE    +    PT +
Sbjct: 34  VFIDRAKGAYVWDVDGKRYIDYVGSWGPAILGHAHPEVVEAVQKQAE--KGLSYGAPTEL 91

Query: 89  RGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGRT---- 144
             E    L   L P ++ V  VNSGTEA   A++ AR  TGR + V    G+ G +    
Sbjct: 92  EVEM-ADLICELIPSVDMVRMVNSGTEATMTAIRLARGATGRDRIVKFEGGYHGHSDSLL 150

Query: 145 --MGSLSVTWEPKYREPFLP--LVEPVEFIPYNDVEALKRAVDE---ETAAVILEPVQGE 197
              GS ++T       P +P  L E    + YND E ++   DE   E A +I+EPV G 
Sbjct: 151 VKAGSGALT-HGVPSSPGVPKCLAEQTLTLTYNDAEQVRNVFDEVGDEIACIIVEPVAGN 209

Query: 198 GGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALG 257
               P  P FL   R++    GA+LI DE+ TG  R G   A   +GI PD+ T  K +G
Sbjct: 210 MNCIPPVPGFLETLRQVCDAHGAILIFDEVMTGF-RVGLTGAQGRYGITPDLTTFGKVIG 268

Query: 258 GGVPLGVAVMREEVARSMPKGG---HGTTFGGNPLAMAAGVAAIRYLERTRLWE 308
           GG+P+G    + E+   +   G      T  GNPLAMAAG+  ++ + +   +E
Sbjct: 269 GGMPVGALGGKREIMSQLAPTGPVYQAGTLSGNPLAMAAGLTTLKRISQPGFFE 322


Lambda     K      H
   0.319    0.137    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 374
Number of extensions: 22
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 395
Length of database: 432
Length adjustment: 31
Effective length of query: 364
Effective length of database: 401
Effective search space:   145964
Effective search space used:   145964
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory